Variant report

Variant	rs9870529
Chromosome Location	chr3:196297047-196297048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr3:196293701-196297089	Hela-S3	cervix:	n/a	n/a
2	ZNF384	chr3:196297005-196297415	K562	blood:	n/a	n/a
3	JUN	chr3:196294719-196297220	K562	blood:	n/a	chr3:196296209-196296218 chr3:196295398-196295407
4	GTF3C2	chr3:196296873-196297497	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:196294811..196297703-chr3:196694216..196696736,3	K562	blood:
2	chr3:196296444..196298332-chr3:196436281..196438974,2	K562	blood:
3	chr3:196253926..196256027-chr3:196295277..196297106,2	K562	blood:
4	chr3:196294271..196297444-chr3:196668008..196671102,3	K562	blood:
5	chr3:196296634..196299111-chr3:196320822..196323637,2	K562	blood:
6	chr3:196294271..196297444-chr3:196668008..196671102,4	K562	blood:
7	chr3:196294935..196297677-chr3:196667748..196670021,2	MCF-7	breast:
8	chr3:196295234..196297248-chr3:196695881..196697586,3	MCF-7	breast:
9	chr3:196295485..196297090-chr3:196694773..196696786,2	MCF-7	breast:
10	chr3:196228351..196232071-chr3:196294107..196297178,4	MCF-7	breast:

No data

Variant related genes	Relation type
WDR53	TF binding region
ENSG00000119227	Chromatin interaction
ENSG00000270170	Chromatin interaction
ENSG00000114503	Chromatin interaction
ENSG00000163961	Chromatin interaction
ENSG00000213358	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11185546	0.93[CEU][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs12485589	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12634928	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12636646	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12636666	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1872353	0.93[CEU][hapmap];0.82[CHB][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs2341337	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34676641	0.94[EUR][1000 genomes]
rs35827219	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66570007	0.90[EUR][1000 genomes]
rs6764637	0.94[EUR][1000 genomes]
rs6791472	0.94[EUR][1000 genomes]
rs6808029	0.93[EUR][1000 genomes]
rs7648453	0.94[EUR][1000 genomes]
rs9825103	0.86[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	nsv1010643	chr3:196288064-196788645	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
12	esv3347483	chr3:196294955-196297053	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9870529	FBXO45	Cis_1M	lymphoblastoid	RTeQTL
rs9870529	RNF168	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196294400-196297200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr3:196294800-196297200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:196296200-196297200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:196296200-196297200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr3:196296200-196297200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:196296200-196297200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:196296200-196297200	Flanking Active TSS	Fetal Brain Female	brain
8	chr3:196296400-196297200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:196296400-196297200	Flanking Active TSS	Fetal Heart	heart
10	chr3:196296400-196297400	Enhancers	Pancreas	Pancrea
11	chr3:196296400-196297400	Flanking Active TSS	Hela-S3	cervix
12	chr3:196296400-196297600	Flanking Active TSS	Dnd41	blood
13	chr3:196296400-196304400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:196296400-196304400	Weak transcription	Lung	lung
15	chr3:196296400-196311000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:196296600-196297200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr3:196296600-196297200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:196296600-196297200	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr3:196296600-196297200	Enhancers	Primary B cells from peripheral blood	blood
20	chr3:196296600-196297200	Enhancers	Primary T cells from cord blood	blood
21	chr3:196296600-196297200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:196296600-196297200	Enhancers	Liver	Liver
23	chr3:196296600-196297200	Enhancers	Stomach Mucosa	stomach
24	chr3:196296600-196297200	Flanking Active TSS	HMEC	breast
25	chr3:196296600-196297400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:196296600-196297400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:196296600-196297400	Enhancers	Fetal Muscle Trunk	muscle
28	chr3:196296600-196297400	Enhancers	Gastric	stomach
29	chr3:196296600-196297400	Flanking Active TSS	NHEK	skin
30	chr3:196296600-196300200	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr3:196296600-196320200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:196296800-196297200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:196296800-196297200	Enhancers	Primary hematopoietic stem cells	blood
34	chr3:196296800-196297200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr3:196296800-196297200	Enhancers	Fetal Stomach	stomach
36	chr3:196296800-196297200	Flanking Active TSS	GM12878-XiMat	blood
37	chr3:196296800-196297400	Enhancers	Primary B cells from cord blood	blood
38	chr3:196296800-196297400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:196296800-196297400	Enhancers	Adipose Nuclei	Adipose
40	chr3:196296800-196297400	Enhancers	Fetal Muscle Leg	muscle
41	chr3:196296800-196297400	Enhancers	Fetal Thymus	thymus
42	chr3:196296800-196297400	Enhancers	Small Intestine	intestine
43	chr3:196296800-196298000	Enhancers	Fetal Brain Male	brain
44	chr3:196296800-196298400	Enhancers	Primary T cells fromperipheralblood	blood
45	chr3:196296800-196299200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:196296800-196299400	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr3:196296800-196299600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:196296800-196305800	Weak transcription	HSMM	muscle
49	chr3:196296800-196311000	Weak transcription	Placenta	Placenta
50	chr3:196296800-196316800	Weak transcription	Right Ventricle	heart

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